Sodium in PDB 6z55: Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070

All present enzymatic activity of Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070:
2.7.12.1;

The structure of Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070, PDB code: 6z55 was solved by A.Chaikuad, P.Benderitter, J.Hoflack, A.Denis, S.Knapp, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.99 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.730, 131.360, 83.800, 90.00, 107.80, 90.00
R / Rfree (%)	15.7 / 19.5

The binding sites of Sodium atom in the Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070 (pdb code 6z55). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070, PDB code: 6z55:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na517 b:27.8 occ:1.00 OD1 A:ASP327 2.8 20.0 1.0 O A:HOH695 2.8 19.8 1.0 O A:THR325 2.8 12.1 1.0 OG1 A:THR280 2.9 11.4 1.0 NE2 A:GLN353 3.3 18.8 1.0 N A:ASP327 3.3 14.5 1.0 N A:THR280 3.4 12.2 1.0 C A:PHE326 3.5 13.8 1.0 O A:GLN278 3.5 17.9 1.0 CB A:THR280 3.6 11.5 1.0 CA A:ASP327 3.7 16.1 1.0 C A:LEU279 3.7 13.9 1.0 C A:THR325 3.8 12.5 1.0 CG A:ASP327 3.9 19.8 1.0 CA A:LEU279 3.9 14.7 1.0 C A:GLN278 4.0 16.9 1.0 CA A:PHE326 4.0 15.4 1.0 CD A:GLN353 4.1 16.0 1.0 O A:PHE326 4.1 14.2 1.0 CA A:THR280 4.1 12.0 1.0 N A:LEU279 4.1 16.0 1.0 N A:PHE326 4.4 13.7 1.0 CB A:ASP327 4.4 16.8 1.0 O A:LEU279 4.4 16.2 1.0 OE1 A:GLN353 4.4 15.6 1.0 NE2 A:HIS331 4.5 14.0 1.0 O A:HOH986 4.7 36.0 1.0 CE1 A:HIS331 4.9 14.2 1.0 CG A:GLN353 5.0 14.3 1.0 OD2 A:ASP327 5.0 22.3 1.0 CG2 A:THR280 5.0 11.8 1.0 CA A:THR325 5.0 12.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na518 b:24.9 occ:0.80 O A:SER132 2.3 23.0 1.0 O A:HOH860 2.4 30.9 1.0 O A:SER135 2.4 27.7 1.0 O2 A:EDO509 2.4 29.5 1.0 O1 A:EDO509 2.4 26.2 1.0 C2 A:EDO509 3.1 28.6 1.0 C1 A:EDO509 3.3 29.6 1.0 C A:SER132 3.4 23.0 1.0 OG A:SER132 3.5 23.9 1.0 C A:SER135 3.6 24.0 1.0 CA A:SER132 3.9 24.8 1.0 CB A:SER135 4.1 24.2 1.0 CG A:ASP150 4.1 20.4 1.0 CA A:SER135 4.2 25.9 1.0 OD1 A:ASP150 4.3 22.9 1.0 N A:SER135 4.3 28.5 1.0 CB A:SER132 4.3 25.5 1.0 OD2 A:ASP150 4.3 20.3 1.0 O A:HOH792 4.3 29.7 1.0 CG2 A:VAL136 4.3 27.2 1.0 CB A:ASP150 4.4 18.5 1.0 N A:SER133 4.5 22.8 1.0 OG A:SER135 4.6 22.1 1.0 O A:TRP151 4.6 17.0 1.0 N A:VAL136 4.7 23.0 1.0 O A:HOH650 4.7 20.0 1.0 CA A:SER133 4.8 23.6 1.0 CA A:VAL136 4.9 23.2 1.0 C A:SER133 5.0 25.6 1.0 O A:HOH712 5.0 26.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na515 b:26.1 occ:1.00 OD1 B:ASP327 2.7 19.1 1.0 O B:HOH694 2.7 20.8 1.0 O B:THR325 2.8 12.5 1.0 OG1 B:THR280 2.9 13.2 1.0 NE2 B:GLN353 3.3 16.0 1.0 N B:ASP327 3.3 13.7 1.0 N B:THR280 3.4 13.2 1.0 C B:PHE326 3.5 13.9 1.0 O B:GLN278 3.5 17.5 1.0 CB B:THR280 3.6 12.9 1.0 C B:LEU279 3.7 15.2 1.0 CA B:ASP327 3.7 14.7 1.0 CG B:ASP327 3.8 18.1 1.0 C B:THR325 3.9 13.5 1.0 CA B:LEU279 3.9 15.6 1.0 C B:GLN278 4.0 17.9 1.0 CA B:PHE326 4.0 15.1 1.0 O B:PHE326 4.1 13.8 1.0 CD B:GLN353 4.1 14.6 1.0 CA B:THR280 4.1 13.0 1.0 N B:LEU279 4.1 16.2 1.0 CB B:ASP327 4.3 15.5 1.0 O B:LEU279 4.4 16.1 1.0 NE2 B:HIS331 4.4 14.8 1.0 N B:PHE326 4.4 13.3 1.0 OE1 B:GLN353 4.5 13.6 1.0 CE1 B:HIS331 4.8 15.2 1.0 OD2 B:ASP327 4.9 21.8 1.0 CG B:GLN353 4.9 14.6 1.0 CG2 B:THR280 5.0 12.3 1.0

A.Chaikuad, P.Benderitter, J.Hoflack, A.Denis, S.Knapp, Structural Genomics Consortium (Sgc). Crystal Structure of CLK3 in Complex with Macrocycle ODS2004070 To Be Published.